This study provides the first comprehensive genome-wide phylogenomic framework for the genus Erwinia, integrating taxonomy, pan-genome diversity, virulence-associated determinants, and mobile genetic elements across all 18 currently recognized species.
Abstract
The genus Erwinia comprises a diverse group of bacteria associated with plants, insects, and the environment, including several economically important phytopathogens. The genus has been revised taxonomically many times, yet a thorough and genome-wide assessment of its evolutionary relationships and genomic diversity has been lacking. In this research, we carried out an extensive phylogenomic and comparative genomic analyses of the genus Erwinia using 104 genomes including historically important strains. Genome-wide analyses integrating average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), core-genome phylogenomics, pan-genome analysis, and comparative genomics resolved evolutionary relationships across the genus and identified multiple taxonomic inconsistencies. The pan-genome analysis revealed a relatively small core genome alongside an extensive accessory genome, underscoring the substantial genomic plasticity and ongoing diversification within the genus. The comparative analyses further showed pronounced lineage-specific variation in secretion systems, exopolysaccharide biosynthetic loci, flagellar gene clusters, genomic islands, prophages, and iron acquisition systems, suggesting that virulence-associated determinants have evolved through differential gene gain, loss, and conservation across distinct lineages, thereby facilitating host and ecological niche adaptation. This lineage-specific variation indicates that pathogenicity in the genus is not driven by a single conserved set of virulence determinants but instead reflects distinct combinations of virulence-associated genes. These findings refine the genomic framework of the genus Erwinia, provide evidence for taxonomic revision of several lineages, and improve our understanding of the evolutionary relationships, genomic diversification, and lineage-specific adaptations associated with host interactions and ecological specialization. Impact Statement This study provides the first comprehensive genome-wide phylogenomic framework for the genus Erwinia, integrating taxonomy, pan-genome diversity, virulence-associated determinants, and mobile genetic elements across all 18 currently recognized species. Analyses resolve evolutionary relationships, uncover multiple taxonomic inconsistencies, identify previously unrecognized species-level lineages, including a putative novel Erwinia species PL328 isolated from Cornus florida (dogwood), and reveal lineage-specific genomic features. These findings establish a valuable genomic foundation for future studies of Erwinia evolution, taxonomy, and plant-microbe interactions. Data Summary Genomes sequenced in this study were submitted to the NCBI database under the accession numbers: JCBCPT000000000
Conordance of codon usage and functional gene abundance with phylogeny is revealed, along with diverse host- and lifestyle-associated adaptive strategies in this important group of plant pathogens.
Jian-Xin Shen, M. Qiao, Jiahao Hong et al.· IMA Fungus· 0 citations
New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Shaima Mahfood Ebrahim Abdulrahman, M. Karaismailoğlu· Bartın University Internatio...· 0 citations
Aquirufa
is a widespread and diverse bacterial genus inhabiting freshwater ecosystems. Analyses of genomes from cultured strains and metagenome-assembled genomes (MAGs) of the genus revealed four phylogenetically distinct branches that differed markedly in the proportions of cultured strains and MAGs they contained. In total, 56 species or species-like taxa were identified, including eight novel species described here. Proteorhodopsin genes were detected in many of the genomes and were found across a wide range of habitat types, but their prevalence differed considerably among the four phylogenetic branches. Detailed analyses of two branches with markedly different proteorhodopsin gene frequencies suggested differences in the occurrence, size, structure, and pangenomes of their populations. Comparative whole-genome analyses showed that proteorhodopsin genes in
Aquirufa
consistently co-occurred with two key genes involved in retinal chromophore biosynthesis. These three genes exhibited distinct evolutionary patterns, most likely reflecting differences in recombination and co-evolution. Phylogenetic analyses placed the
Aquirufa
proteorhodopsins within the proteorhodopsin-xanthorhodopsin clade, specifically in a lineage comprising proteorhodopsins from species of the phylum
Bacteroidota
. Extending the analyses to related proteorhodopsins revealed additional patterns. Thirteen distinct gene arrangement types and all three common spectral-tuning residues were identified, with variation occurring not only among genera but occasionally even among species within the same genus. Overall, our findings indicated that the evolution, acquisition, horizontal transfer, and recombination of proteorhodopsin genes and associated genes have proceeded differently across taxonomic groups.
Alexandra Pitt, Stefan Lienbacher, J. Schmidt et al.· Microbial Ecology· 0 citations
Limeum is the sole genus of Limeaceae, comprising approximately 20 species distributed across Africa, Southwest Asia, and India. However, genomic resources for the family are limited, and phylogenetic relationships within the genus remain poorly understood. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of six Limeum species to investigate their genomic characteristics and phylogenetic relationships. The chloroplast genomes ranged from 156,354 bp to 160,377 bp in length and exhibited the typical quadripartite structure. Each genome contained 131 genes, consisting of 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analyses identified 455 tandem repeats and 616 simple sequence repeats, revealing 16 highly variable regions that may serve as potential molecular markers for future studies. Phylogenetic analyses based on complete chloroplast genome sequences strongly supported the monophyly of Limeum and robustly resolved interspecific relationships within the genus. These results provide the first comprehensive plastome dataset for Limeum and a valuable genomic resource for species identification, genetic diversity assessment, phylogenetic reconstruction, and evolution studies of Limeum and the family Limeaceae.
Zheng-Lin He, Jin-Fei Xiao, Fei Zhao et al.· Korean Journal of Plant Taxo...· 0 citations
This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.
Gang Lu, Mengmeng Yu, Fazu Xu et al.· PeerJ· 0 citations
Background: The genus Anomala is exceptionally species-rich and includes many species recognized as major agricultural and forest pests. Nevertheless, the taxonomic status of certain species remains contentious, and the phylogenetic relationships within the genus are still poorly resolved and in need of further investigation. Objectives: To better elucidate the evolutionary relationships among these insects, we assembled the complete mitochondrial genomes (mitogenomes) of four Anomala species—A. aulax, Anomala sp., A. vitalisi, and A. xantholoma. Multiple molecular datasets were integrated to reconstruct the phylogenetic framework of Scarabaeidae. Methods: Wild adult specimens of four Anomala species were collected. After total DNA extraction, complete mitogenomes were assembled and annotated for comparative analysis of core genomic traits. Multiple datasets were applied to construct phylogenetic trees via maximum likelihood and Bayesian inference, so as to evaluate the evolutionary characteristics of each taxon. Results: Our analyses reveal that the mitogenomes of Anomala species exhibit a conserved architecture, characterized by similarities in genome size, AT nucleotide bias, and gene order, suggesting a high degree of evolutionary stability within the genus. The resulting phylogenetic trees robustly support the monophyly of the following families: Passalidae, Lucanidae, Geotrupidae, Trogidae, Hybosoridae, and Glaphyridae. Additionally, the phylogenetic findings revealed the paraphyly of both Scarabaeidae and Anomala, and further suggested that Melolonthinae is likely a paraphyletic group. Conclusions: This study enriches the currently available mitogenomic data and provides a preliminary foundation for understanding the phylogeny, resource conservation, and genetic diversity of Anomala.
